Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi

Summary: The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC ('EPIC') array from Illumina. We discuss methods for the joint analysis and normalization of data from the HumanMethylation450 ('450k') and EPIC platforms. We introduce the single-sample Noob ( ssNoob ) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of Infinium methylation arrays. We show how to use reference 450k datasets to estimate cell type composition of samples on EPIC…

• TC
  Tower Cancer Research Foundation
• NI
  National Institutes of Health

  Award: U24CA180996
• NC
  National Cancer Institute

  Award: U24CA180996